changeset 1:8164dae8b281 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Prepare_Ssuis_serotypingPipeline.py	Thu May 09 04:14:32 2019 -0400
@@ -0,0 +1,82 @@
+#!/usr/bin/python
+#-*- coding: utf-8 -*-
+#Libraries:
+import os, os.path, argparse, sys, gzip, re
+
+
+
+##### MAIN
+def __main__():
+  ### Arguments:
+  parser = argparse.ArgumentParser(description='''Launch Ssuis_serotypingPipeline.pl with correct argument''', epilog="""This script needs few options use -h to see it.""")
+
+  parser.add_argument('--fastq_file', dest='ffile')
+  parser.add_argument('--scoreName', dest='sname')
+  parser.add_argument('--output2', dest='o2')
+  parser.add_argument('--output3', dest='o3')
+  parser.add_argument('--output4', dest='o4')
+  parser.add_argument('--output5', dest='o5')
+  parser.add_argument('--output6', dest='o6')
+  parser.add_argument('--output7', dest='o7')
+  parser.add_argument('--output8', dest='o8')
+  parser.add_argument('--serotype_db', dest='sd')
+  parser.add_argument('--serotype_definitions', dest='sdef')
+  parser.add_argument('--cps2K', dest='cps')
+  parser.add_argument('--Virulence_db', dest='Vdb')
+  parser.add_argument('--recN_db', dest='recdb')
+  parser.add_argument('--MLST_definitions', dest='MLSTdef')
+  parser.add_argument('--MLST_db', dest='MLSTdb') 
+  parser.add_argument('--ends', dest='ends')
+  parser.add_argument('--forward', dest='f')
+  parser.add_argument('--reverse', dest='r')
+
+  ### Get argument in variable:
+  options = parser.parse_args()
+  ffile = options.ffile
+  sname = options.sname
+  output2 = options.o2
+  output3 = options.o3
+  output4 = options.o4
+  output5 = options.o5
+  output6 = options.o6
+  output7 = options.o7
+  output8 = options.o8
+  sd = options.sd
+  sdef = options.sdef
+  cps = options.cps
+  Vdb = options.Vdb
+  recdb = options.recdb
+  MLSTdef = options.MLSTdef
+  MLSTdb = options.MLSTdb
+  ends = options.ends
+  f = options.f
+  r = options.r
+  
+  way_pipeline = "/results/anses/bin/SsuisSerotyping_pipeline/"
+  input_path = os.path.splitext(output2)[0]+"_input_file_test/"
+  output_path = os.path.splitext(output2)[0]+"_Results/"
+  os.system("mkdir -p "+input_path)
+  os.system("cp "+ffile+" "+input_path+"/file_test.fastq") 
+  fdir = input_path
+
+  if ends == "se":
+    f = "SINGLE"
+    r = "SINGLE"
+
+  if sd is None:
+    os.system("perl "+way_pipeline+"/Ssuis_serotypingPipeline.pl --fastq_directory "+str(fdir)+" --scoreName "+output_path+"Results --ends "+str(ends)+" --forward "+str(f)+" --reverse "+str(r))
+  else:
+    os.system("perl "+way_pipeline+"/Ssuis_serotypingPipeline.pl --fastq_directory "+str(fdir)+" --scoreName "+output_path+"Results --serotype_db "+str(sd)+" --serotype_definitions "+str(sdef)+" --cps2K "+str(cps)+" --Virulence_db "+str(Vdb)+" --recN_db "+str(recdb)+" --MLST_definitions "+str(MLSTdef)+" --MLST_db "+str(MLSTdb)+" --ends "+str(ends)+" --forward "+str(f)+" --reverse "+str(r))
+  
+  os.system("rm -r "+fdir)
+  os.system("mv "+output_path+"/Results_FinalResults.txt "+sname)
+  os.system("mv "+output_path+"/Results_MLSTResults.txt "+output2)
+  os.system("mv "+output_path+"/Results_recN__fullgenes__recN_full__results.txt "+output3)
+  os.system("mv "+output_path+"/Results_speciesConfirmation.txt "+output4)
+  os.system("mv "+output_path+"/Results_FinalSerotypingResults.txt "+output5)
+  os.system("mv "+output_path+"/Results_InitialCapsuleResults.txt "+output6)
+  os.system("mv "+output_path+"/Results_VirulenceFactors__fullgenes__Virulence__results.txt "+output7)
+  os.system("mv "+output_path+"/Results_VirulenceFactorResults.txt "+output8)
+#### MAIN END
+if __name__ == "__main__": __main__() 
+